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What is the .HMM File Extension?


.HMM File Extension Description:

HMMER is software that implements the profile of Hidden Markov Models (HMM) for biological sequence analysis. The profile are calculated from multiple sequence alignment data and are stored in the Profile HMM file format that usually ends with the HMM file extension.

The file with the .hmm file extension is an ASCII file that contains a lot of headers and descriptive records as well as large numerical templates that hold the model motif. This file can include one or more HMMs, each of which begins with an identifier that provides backward compatibility as the HMMER application is being modified and closes with // that provides multiple HMMs to be linked together into a single HMM database file.

Each file with the .hmm file extension is divided into two sections: the first one contains text information and different parameters in a tag-value schema ended by a line that begins with HMM whereas the second one is more of a fixed whitespace containing the key model parameters ended by the // closing the complete definition for a single profile HMM.

After the identifier, each line in the header section of the file with the .hmm file extension is a single tag of five characters or less. Thus, the first six characters of these lines can be held in reserve for the tag and the space while the rest of the line begins on the seventh character.

The first line in the main model section of this file contains three fields:

* first field - contains score for 1-t(B!D)

* second field - does not contain B!I transition; value is always *

* third field - contains the score for the t(B!D).

These fields can be used for changes from the B state into the first node of the model. Theoretically, the third is the only field needed to obtain t(B!D) but in practice, both the first and the third fields are read by HMMER, which are then converted into probabilities, and finally renormalized to obtain t(B!D). The rest of the model consists of three lines for each node, namely Match Emission, Insert Emission, and State Transition.

Author: HMMER
Author URL: http://www.hmmer.wustl.edu
Related Applications: HMMER
Common Path: N/A

Recommendation:

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Do you have errors with .HMM files?

What Causes .HMM files Errors?

When you encounter errors with .HMM files you are potential experiencing a severe Windows registry error - this error may be the result of corruption in your program registry and you should act to fix it at once to prevent further damage to the registry. Having these errors places your computer in danger for fatal crashes, blue screen errors as well as system device failure.

.HMM files Errors - Common Symptoms:

.HMM files errors bring forth many symptoms, such as: pc locks while shutting down or starting up, programs crash, reduced personal computer speed, case speaker beeping, problems saving documents, sluggish behaviour and failure while installing programs.

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